Using Computing Resources

Transcription

1 Using Computing Resources I. Timofeyev University of Houston September 2018

2 NEVER give your password to anyone; NEVER reply to any s requesting your password Contacting sysadmin: Your Desktop: linux based machine Learn linux: the joy of the terminal window Editors: emacs (separate window editor) and vi (within terminal window) aliases: edit your.cshrc or.bashrc Command Line programs and utilities Each computer has a local disk Your home directory is located on the department server and all file changes are transferred over the network your home directory is automatically mounted compute01 136:/home/ilya>pwd /home/ilya

3 Linux Commands List all files >ls Make Directory >mkdir dir name Change Directory >cd dir name Go to home directory >cd Go one directory up >cd.. Running in the background, use &: >matlab & Storage 5GB in the home volume (/home/$user or ~) 20GB in the storage volume (/storage/$user or ~/servers/storage) 2GB in the web volume (/www/$user or ~/storage/www)

4 Linux Commands Local Machine: your desktop machine Remote Machine: you have access to other machines in the department ssh2 139:/home/ilya> ssh ld65 Last login: Wed Sep 26 11:25: Login to compute** machine ~]$ ssh compute01 Last login: Thu Sep 27 19:53: from ~]$ pwd /home/ilya ~]$ ~]$ cd compute01 140:/home/ilya> Access from a Laptop Mac: you should have ssh already PC: you can emulate linux by installing cygwin

5 ssh and sftp You can create alias alias sshuh= ssh you need another program to transfer files between UH account and your laptop sftp or putty can be used alias sftpuh= sftp sftp has its own command line interface You should compress files before transfer >zip -r my.zip <dir name> >sftpuh sftp>get my.zip or sftp>put my.zip >unzip my.zip

6 Running jobs on compute** machines compute-status ld65 145:/home/ilya> compute-status host cpus load compute compute compute compute compute compute compute compute total_cpus free_cpus utilization

7 Running jobs on compute** machines You have to run your jobs on \scratch ld65 146:/home/ilya> ld65 146:/home/ilya> ssh compute02 ~]$ cd /scratch compute02 144:/scratch> ls adrian/ cx/ mock/ schiu/ torok/ aguo/ jsa/ pan/ yushutin/ bhargav/ jsalcala/ pxzfile/ compute02 145:/scratch> mkdir ilya compute02 146:/scratch> cd ilya compute02 147:/scratch/ilya> Transfer your data into your home directory when you re done zip your files before copying

8 Running jobs on compute** machines To see all jobs running >top Nice your jobs >nice +15 <pid> Run your jobs in the background, redirect output, no figures in matlab or python Running Matlab >nohup matlab -nodisplay -nodesktop -nojvm -nosplash < my.m > out.txt & alias runmatlab nohup matlab -nodisplay -nodesktop -nojvm - >runmatlab < my.m > out.txt & save your data in matlab save( mydata.mat ); Put exit; at the end No Figures

9 Running python on compute** machines Write python program Background running - use nohup, redirect output, renice your program, no plotting compute01 186:/scratch/ilya/run1> nohup python3 < oumc2.py > out.txt & [1] compute01 187:/scratch/ilya/run1> ps PID TTY TIME CMD pts/5 00:00:00 tcsh pts/5 00:00:14 python pts/5 00:00:00 ps compute01 188:/scratch/ilya/run1> renice (process ID) old priority 0, new priority 15 compute01 189:/scratch/ilya/run1>

10 Killing programs compute01 190:/scratch/ilya/run1> kill compute01 191:/scratch/ilya/run1> [1] Killed python3 < oumc2.py > out.tx compute01 191:/scratch/ilya/run1>